Combining speed control and transform effect strips
It's hard to tell what you're asking without some pictures, but I think you're adding all the effects strips to the original footage. This doesn't work when you're trying to combine more than one effect on the same section of footage. See the following example:



In this (contrived) example, I have a Gamma Cross, a Transform, and a Glow effect that I want to all be applied to that transition between the two strips. If you select one of the purple strips and add each effect to it, then the only effect that will actually be applied is whatever effect is on top.

In order to have all the effects combined the way you expect, you would add the Gamma Cross like normal, then select the Gamma Cross and add the Transform to the Gamma Cross strip, then select the Transform and add the Glow to the Transform strip. This will make each effect combine with the others the way you'd expect them to.